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An optimization algorithm for dose reduction with fluence-modulated proton CT.

Dickmann J, Rit S, Pankuch M, Johnson RP, Schulte RW, Parodi K, Dedes G, Landry G.

Med Phys. 2020 Feb 10. doi: 10.1002/mp.14084. [Epub ahead of print]


Serendipitous Rediscovery of the Facile Cyclization of Z,Z-3,5-Octadiene-1,7-diyne Derivatives to Afford Stable, Substituted Naphthocyclobutadienes.

Barker JE, Kodama T, Song MK, Frederickson CK, Jousselin-Oba T, Zakharov LN, Marrot J, Frigoli M, Johnson RP, Haley MM.

Chempluschem. 2019 Jun;84(6):665-672. doi: 10.1002/cplu.201800605. Epub 2019 Jan 23.


Synthesis of Oligo(1,8-pyrenylene)s: A Series of Functional Molecular Liquids.

Walsh JC, Hogan DT, Williams KM, Brake SD, Venkataramana G, Misener TA, Wallace BJ, Johnson RP, Thompson DW, Zhao Y, Wagner BD, Bodwell GJ.

Chempluschem. 2019 Jun;84(6):754-765. doi: 10.1002/cplu.201900133. Epub 2019 May 9.


Effect of a bacteriophage T5virus on growth of Shiga toxigenic Escherichia coli and Salmonella strains in individual and mixed cultures.

Niu YD, Liu H, Johnson RP, McAllister TA, Stanford K.

Virol J. 2020 Jan 7;17(1):3. doi: 10.1186/s12985-019-1269-7.


Acid-catalyzed rearrangements in arenes: interconversions in the quaterphenyl series.

Skraba-Joiner SL, Holt CJ, Johnson RP.

Beilstein J Org Chem. 2019 Nov 6;15:2655-2663. doi: 10.3762/bjoc.15.258. eCollection 2019.


Antigenic competition in CD4+ T cell responses in a randomized, multicenter, double-blind clinical HIV vaccine trial.

Kallas EG, Grunenberg NA, Yu C, Manso B, Pantaleo G, Casapia M, Baden LR, Valencia J, Sobieszczyk M, Van Tieu H, Allen M, Hural J, Graham BS, Kublin J, Gilbert PB, Corey L, Goepfert PA, McElrath MJ, Johnson RP, Huang Y, Frahm N.

Sci Transl Med. 2019 Nov 20;11(519). pii: eaaw1673. doi: 10.1126/scitranslmed.aaw1673.


Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

Tyson S, Peterson CL, Olson A, Tyler S, Knox N, Griffiths E, Dooley D, Hsiao W, Cabral J, Johnson RP, Laing C, Gannon V, Lynch T, Van Domselaar G, Brinkman F, Graham M.

Microbiol Resour Announc. 2019 Oct 10;8(41). pii: e00625-19. doi: 10.1128/MRA.00625-19.


Hyperbaric oxygen is still needed in the management and prevention of mandibular necrosis: a response to Mr. Richard Clarke.

Marx RE, Feldmeier JJ, Johnson RP.

Undersea Hyperb Med. 2019 Jun-Jul-Aug - Third Quarter;46(4):399-408.


Effect of calcium glucoheptonate on proliferation and osteogenesis of osteoblast-like cells in vitro.

Modi PK, Prabhu A, Bhandary YP, Shenoy P S, Hegde A, Es SP, Johnson RP, Das SP, Vazirally S, Rekha PD.

PLoS One. 2019 Sep 9;14(9):e0222240. doi: 10.1371/journal.pone.0222240. eCollection 2019.


A Short and Efficient Synthesis of the [3]Triangulene Ring System.

Holt CJ, Wentworth KJ, Johnson RP.

Angew Chem Int Ed Engl. 2019 Oct 28;58(44):15793-15796. doi: 10.1002/anie.201907226. Epub 2019 Sep 24.


Altered differentiation is central to HIV-specific CD4+ T cell dysfunction in progressive disease.

Morou A, Brunet-Ratnasingham E, Dubé M, Charlebois R, Mercier E, Darko S, Brassard N, Nganou-Makamdop K, Arumugam S, Gendron-Lepage G, Yang L, Niessl J, Baxter AE, Billingsley JM, Rajakumar PA, Lefebvre F, Johnson RP, Tremblay C, Routy JP, Wyatt RT, Finzi A, Douek DC, Kaufmann DE.

Nat Immunol. 2019 Aug;20(8):1059-1070. doi: 10.1038/s41590-019-0418-x. Epub 2019 Jul 15.


Experimental comparison of proton CT and dual energy x-ray CT for relative stopping power estimation in proton therapy.

Dedes G, Dickmann J, Niepel K, Wesp P, Johnson RP, Pankuch M, Bashkirov V, Rit S, Volz L, Schulte RW, Landry G, Parodi K.

Phys Med Biol. 2019 Aug 14;64(16):165002. doi: 10.1088/1361-6560/ab2b72.


Improving single-event proton CT by removing nuclear interaction events within the energy/range detector.

Volz L, Piersimoni P, Johnson RP, Bashkirov VA, Schulte RW, Seco J.

Phys Med Biol. 2019 Aug 1;64(15):15NT01. doi: 10.1088/1361-6560/ab2671.


Prediction of image noise contributions in proton computed tomography and comparison to measurements.

Dickmann J, Wesp P, Rädler M, Rit S, Pankuch M, Johnson RP, Bashkirov V, Schulte RW, Parodi K, Landry G, Dedes G.

Phys Med Biol. 2019 Jul 16;64(14):145016. doi: 10.1088/1361-6560/ab2474.


CPHLN recommendations for the laboratory detection of Shiga toxin-producing Escherichia coli (O157 and non-O157).

Chui L, Christianson S, Alexander DC, Arseneau V, Bekal S, Berenger B, Chen Y, Davidson R, Farrell DJ, German GJ, Gilbert L, Hoang L, Johnson RP, MacKeen A, Maki A, Nadon C, Nickerson E, Peralta A, Arneson SR, Yu Y, Ziebell K.

Can Commun Dis Rep. 2018 Nov 1;44(11):304-307. doi: 10.14745/ccdr.v44i11a06. eCollection 2018 Nov 1.


Gene Regulatory Programs Conferring Phenotypic Identities to Human NK Cells.

Collins PL, Cella M, Porter SI, Li S, Gurewitz GL, Hong HS, Johnson RP, Oltz EM, Colonna M.

Cell. 2019 Jan 10;176(1-2):348-360.e12. doi: 10.1016/j.cell.2018.11.045. Epub 2018 Dec 27.


Targeting discriminatory SNPs in Salmonella enterica serovar Heidelberg genomes using RNase H2-dependent PCR.

Labbé G, Rankin MA, Robertson J, Moffat J, Giang E, Lee LK, Ziebell K, MacKinnon J, Laing CR, Parmley EJ, Agunos A, Daignault D, Bekal S, Chui L, MacDonald KA, Hoang L, Slavic D, Ramsay D, Pollari F, Nash JHE, Johnson RP.

J Microbiol Methods. 2019 Feb;157:81-87. doi: 10.1016/j.mimet.2018.12.021. Epub 2018 Dec 25.


Shiga Toxin/Lipopolysaccharide Activates Caspase-4 and Gasdermin D to Trigger Mitochondrial Reactive Oxygen Species Upstream of the NLRP3 Inflammasome.

Platnich JM, Chung H, Lau A, Sandall CF, Bondzi-Simpson A, Chen HM, Komada T, Trotman-Grant AC, Brandelli JR, Chun J, Beck PL, Philpott DJ, Girardin SE, Ho M, Johnson RP, MacDonald JA, Armstrong GD, Muruve DA.

Cell Rep. 2018 Nov 6;25(6):1525-1536.e7. doi: 10.1016/j.celrep.2018.09.071.


Developing quality assurance practices and measures for implementing and sustaining the Transition to Independence Process (TIP) model.

Klodnick VV, Clark HBR, Johnson RP, Fagan MA.

Psychiatr Rehabil J. 2019 Mar;42(1):71-78. doi: 10.1037/prj0000324. Epub 2018 Sep 27.


Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study.

Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ.

Front Microbiol. 2018 Aug 31;9:2040. doi: 10.3389/fmicb.2018.02040. eCollection 2018.


The impact of secondary fragments on the image quality of helium ion imaging.

Volz L, Piersimoni P, Bashkirov VA, Brons S, Collins-Fekete CA, Johnson RP, Schulte RW, Seco J.

Phys Med Biol. 2018 Oct 2;63(19):195016. doi: 10.1088/1361-6560/aadf25.


Polymorphisms in Rhesus Macaque Tetherin Are Associated with Differences in Acute Viremia in Simian Immunodeficiency Virus Δnef-Infected Animals.

Janaka SK, Tavakoli-Tameh A, Neidermyer WJ Jr, Serra-Moreno R, Hoxie JA, Desrosiers RC, Johnson RP, Lifson JD, Wolinsky SM, Evans DT.

J Virol. 2018 Oct 29;92(22). pii: e00542-18. doi: 10.1128/JVI.00542-18. Print 2018 Nov 15.


Experimental fluence-modulated proton computed tomography by pencil beam scanning.

Dedes G, Johnson RP, Pankuch M, Detrich N, Pols WMA, Rit S, Schulte RW, Parodi K, Landry G.

Med Phys. 2018 Jul;45(7):3287-3296. doi: 10.1002/mp.12989. Epub 2018 Jun 8.


Postnatal Zika virus infection is associated with persistent abnormalities in brain structure, function, and behavior in infant macaques.

Mavigner M, Raper J, Kovacs-Balint Z, Gumber S, O'Neal JT, Bhaumik SK, Zhang X, Habib J, Mattingly C, McDonald CE, Avanzato V, Burke MW, Magnani DM, Bailey VK, Watkins DI, Vanderford TH, Fair D, Earl E, Feczko E, Styner M, Jean SM, Cohen JK, Silvestri G, Johnson RP, O'Connor DH, Wrammert J, Suthar MS, Sanchez MM, Alvarado MC, Chahroudi A.

Sci Transl Med. 2018 Apr 4;10(435). pii: eaao6975. doi: 10.1126/scitranslmed.aao6975.


Vaccine-Associated Maintenance of Epithelial Integrity Correlated With Protection Against Virus Entry.

Shang L, Smith AJ, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Southern PJ, Johnson RP, Carlis JV, Haase AT.

J Infect Dis. 2018 Sep 8;218(8):1272-1283. doi: 10.1093/infdis/jiy062.


Acid-Catalyzed Skeletal Rearrangements in Arenes: Aryl versus Alkyl Ring Pirouettes in Anthracene and Phenanthrene.

Skraba-Joiner SL, Brulet JW, Song MK, Johnson RP.

J Org Chem. 2017 Dec 15;82(24):13076-13083. doi: 10.1021/acs.joc.7b02058. Epub 2017 Nov 22.


Biomimetic Total Synthesis of (±)-Griffipavixanthone via a Cationic Cycloaddition-Cyclization Cascade.

Reichl KD, Smith MJ, Song MK, Johnson RP, Porco JA Jr.

J Am Chem Soc. 2017 Oct 11;139(40):14053-14056. doi: 10.1021/jacs.7b09265. Epub 2017 Oct 2.


Review of medical radiography and tomography with proton beams.

Johnson RP.

Rep Prog Phys. 2018 Jan;81(1):016701. doi: 10.1088/1361-6633/aa8b1d. Review.


Vaccine-modified NF-kB and GR signaling in cervicovaginal epithelium correlates with protection.

Shang L, Smith AJ, Reilly CS, Duan L, Perkey KE, Wietgrefe S, Zupancic M, Southern PJ, Johnson RP, Carlis JV, Haase AT.

Mucosal Immunol. 2018 Mar;11(2):512-522. doi: 10.1038/mi.2017.69. Epub 2017 Aug 9.


Laser-plasmas in the relativistic-transparency regime: Science and applications.

Fernández JC, Cort Gautier D, Huang C, Palaniyappan S, Albright BJ, Bang W, Dyer G, Favalli A, Hunter JF, Mendez J, Roth M, Swinhoe M, Bradley PA, Deppert O, Espy M, Falk K, Guler N, Hamilton C, Hegelich BM, Henzlova D, Ianakiev KD, Iliev M, Johnson RP, Kleinschmidt A, Losko AS, McCary E, Mocko M, Nelson RO, Roycroft R, Santiago Cordoba MA, Schanz VA, Schaumann G, Schmidt DW, Sefkow A, Shimada T, Taddeucci TN, Tebartz A, Vogel SC, Vold E, Wurden GA, Yin L.

Phys Plasmas. 2017 May;24(5):056702. doi: 10.1063/1.4983991. Epub 2017 May 30.


Application of fluence field modulation to proton computed tomography for proton therapy imaging.

Dedes G, De Angelis L, Rit S, Hansen D, Belka C, Bashkirov V, Johnson RP, Coutrakon G, Schubert KE, Schulte RW, Parodi K, Landry G.

Phys Med Biol. 2017 Jul 12;62(15):6026-6043. doi: 10.1088/1361-6560/aa7734.


Bim expression in endothelial cells and pericytes is essential for regression of the fetal ocular vasculature.

Wang S, Zaitoun IS, Johnson RP, Jamali N, Gurel Z, Wintheiser CM, Strasser A, Lindner V, Sheibani N, Sorenson CM.

PLoS One. 2017 May 26;12(5):e0178198. doi: 10.1371/journal.pone.0178198. eCollection 2017.


Strength and Viscosity Effects on Perturbed Shock Front Stability in Metals.

Opie S, Loomis E, Peralta P, Shimada T, Johnson RP.

Phys Rev Lett. 2017 May 12;118(19):195501. doi: 10.1103/PhysRevLett.118.195501. Epub 2017 May 9.


Subtyping of Canadian isolates of Salmonella Enteritidis using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) alone and in combination with Pulsed-Field Gel Electrophoresis (PFGE) and phage typing.

Ziebell K, Chui L, King R, Johnson S, Boerlin P, Johnson RP.

J Microbiol Methods. 2017 Aug;139:29-36. doi: 10.1016/j.mimet.2017.04.012. Epub 2017 Apr 26.


Evidence for the benefits of food chain interventions on E. coli 0157:H7/NM prevalence in retail ground beef and human disease incidence: A success story.

Pollari F, Christidis T, Pintar KDM, Nesbitt A, Farber J, Lavoie MC, Gill A, Kirsch P, Johnson RP.

Can J Public Health. 2017 Apr 20;108(1):e71-e78. doi: 10.17269/cjph.108.5655.


A Retrospective Case-Matched Cost Comparison of Surgical Treatment of Melanoma and Nonmelanoma Skin Cancer in the Outpatient Versus Operating Room Setting.

Johnson RP, Butala N, Alam M, Lawrence N.

Dermatol Surg. 2017 Jul;43(7):897-901. doi: 10.1097/DSS.0000000000001069.


Distinct transcriptome profiles of Gag-specific CD8+ T cells temporally correlated with the protection elicited by SIVΔnef live attenuated vaccine.

Lu W, Wan Y, Ma F, Johnson RP, Li Q.

PLoS One. 2017 Mar 23;12(3):e0173929. doi: 10.1371/journal.pone.0173929. eCollection 2017.


Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine.

Johnson RP, Fleming AM, Perera RT, Burrows CJ, White HS.

J Am Chem Soc. 2017 Feb 22;139(7):2750-2756. doi: 10.1021/jacs.6b12284. Epub 2017 Feb 13.


Dynamic Modulation of Expression of Lentiviral Restriction Factors in Primary CD4+ T Cells following Simian Immunodeficiency Virus Infection.

Rahmberg AR, Rajakumar PA, Billingsley JM, Johnson RP.

J Virol. 2017 Mar 13;91(7). pii: e02189-16. doi: 10.1128/JVI.02189-16. Print 2017 Apr 1.


Software platform for simulation of a prototype proton CT scanner.

Giacometti V, Bashkirov VA, Piersimoni P, Guatelli S, Plautz TE, Sadrozinski HF, Johnson RP, Zatserklyaniy A, Tessonnier T, Parodi K, Rosenfeld AB, Schulte RW.

Med Phys. 2017 Mar;44(3):1002-1016. doi: 10.1002/mp.12107.


Evidence for the benefits of food chain interventions on E. coli O157:H7/NM prevalence in retail ground beef and human disease incidence: A success story.

Pollari F, Christidis T, Pintar KDM, Nesbitt A, Farber J, Lavoie MC, Gill A, Kirsch P, Johnson RP.

Can J Public Health. 2017 Jan;108(1):e71-e78. doi: 10.17269/CJPH.108.5655. Epub 2017 Jan 1.


Persistent Low-Level Replication of SIVΔnef Drives Maturation of Antibody and CD8 T Cell Responses to Induce Protective Immunity against Vaginal SIV Infection.

Adnan S, Reeves RK, Gillis J, Wong FE, Yu Y, Camp JV, Li Q, Connole M, Li Y, Piatak M Jr, Lifson JD, Li W, Keele BF, Kozlowski PA, Desrosiers RC, Haase AT, Johnson RP.

PLoS Pathog. 2016 Dec 13;12(12):e1006104. doi: 10.1371/journal.ppat.1006104. eCollection 2016 Dec.


An evaluation of spatial resolution of a prototype proton CT scanner.

Plautz TE, Bashkirov V, Giacometti V, Hurley RF, Johnson RP, Piersimoni P, Sadrozinski HF, Schulte RW, Zatserklyaniy A.

Med Phys. 2016 Dec;43(12):6291.


Operation of the Preclinical Head Scanner for Proton CT.

Sadrozinski HF, Geoghegan T, Harvey E, Johnson RP, Plautz TE, Zatserklyaniy A, Bashkirov V, Hurley RF, Piersimoni P, Schulte RW, Karbasi P, Schubert KE, Schultze B, Giacometti V.

Nucl Instrum Methods Phys Res A. 2016 Sep 21;831:394-399. Epub 2016 Feb 7.


Magnitude and Quality of Cytokine and Chemokine Storm during Acute Infection Distinguish Nonprogressive and Progressive Simian Immunodeficiency Virus Infections of Nonhuman Primates.

Keating SM, Heitman JW, Wu S, Deng X, Stacey AR, Zahn RC, de la Rosa M, Finstad SL, Lifson JD, Piatak M Jr, Gauduin MC, Kessler BM, Ternette N, Carville A, Johnson RP, Desrosiers RC, Letvin NL, Borrow P, Norris PJ, Schmitz JE.

J Virol. 2016 Oct 28;90(22):10339-10350. doi: 10.1128/JVI.01061-16. Print 2016 Nov 15.


Reproducing SIVΔnef vaccine correlates of protection: trimeric gp41 antibody concentrated at mucosal front lines.

Voss JE, Macauley MS, Rogers KA, Villinger F, Duan L, Shang L, Fink EA, Andrabi R, Colantonio AD, Robinson JE, Johnson RP, Burton DR, Haase AT.

AIDS. 2016 Oct 23;30(16):2427-2438.


Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin.

Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS.

Faraday Discuss. 2016 Dec 12;193:471-485.


Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.

Labbé G, Ziebell K, Bekal S, Macdonald KA, Parmley EJ, Agunos A, Desruisseau A, Daignault D, Slavic D, Hoang L, Ramsay D, Pollari F, Robertson J, Nash JH, Johnson RP.

Genome Announc. 2016 Sep 15;4(5). pii: e00990-16. doi: 10.1128/genomeA.00990-16.


Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia coli in Feces of Western-Canadian Slaughter Cattle.

Stanford K, Johnson RP, Alexander TW, McAllister TA, Reuter T.

PLoS One. 2016 Aug 2;11(8):e0159866. doi: 10.1371/journal.pone.0159866. eCollection 2016.

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